Link OTUs in the HNA population to Productivity

Investigate composition of HNA/LNA populations and relate them to the productivity of Muskegon Lake

Abundance Filtering: 11 OTUs

On Wednesday, April 5th @prubbens ran an analysis without the three outliers. His analysis is in analysis_prod2_remov_outliers.ipynb and pulled out the following 11 OTUs that are associated with heterotrophic productivity:

OTU	Phylum	Class	Order	Family	Genus	Species
Otu000016	Proteobacteria	Betaproteobacteria	Burkholderiales	betII	Pnec	PnecB
Otu000025	Bacteroidetes	Cytophagia	Cytophagales	bacIII	bacIII-A	Unclassified
Otu000034	Verrucomicrobia	Opitutae	Opitutae_vadinHA64	Opitutae_vadinHA64_unclassified	Unclassified	Unclassified
Otu000040	Verrucomicrobia	Verrucomicrobia_unclassified	Verrucomicrobia_unclassified	Verrucomicrobia_unclassified	Verrucomicrobia_unclassified	Unclassified
Otu000041	Verrucomicrobia	[Spartobacteria]	[Chthoniobacterales]	verI-B	Xip-B1	Unclassified
Otu000042	Planctomycetes	Phycisphaerae	Phycisphaerales	Phycisphaeraceae	CL500-3	Unclassified
Otu000050	Planctomycetes	Phycisphaerae	Phycisphaerales	Phycisphaeraceae	CL500-3	Unclassified
Otu000067	Bacteroidetes	Flavobacteriia	Flavobacteriales	bacII	bacII-A	Unclassified
Otu000082	Chlorobi	Chlorobia	Chlorobiales	OPB56	Unclassified	Unclassified
Otu000176	Proteobacteria	Deltaproteobacteria	Bdellovibrionales	Bacteriovoracaceae	Peredibacter	Unclassified
Otu000219	Proteobacteria	Betaproteobacteria	Burkholderiales	betIII	betIII-A	betIII-A1

CorrFilt: 3 OTUs

On Wednesday, April 5th @prubbens ran an analysis without the three outliers and with an additional correlational filtering step. His analysis is in analysis_prod2_corrfiltering.ipynb and pulled out the following 3 OTUs that are associated with heterotrophic productivity:

OTU	Phylum	Class	Order	Family	Genus	Species
Otu000060	Proteobacteria	Alphaproteobacteria	Sphingomonadales	alfIV	alfIV_unclassified	Unclassified
Otu000357	Proteobacteria	Betaproteobacteria	Burkholderiales	betI	betI-B	Rhodo
Otu000124	Verrucomicrobia	Opitutae	Opitutales	Opitutaceae	Opitutus	Unclassified

Figure 1

Figure 2

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Randomized Lasso

On March 17th, @prubbens performed a randomized lasso in analysis_prod2.ipynb that pulled out the following 12 OTUs that are associated with heterotrophic productivity:

The taxonomy associated with the above OTUs (from data/Chloroplasts_removed/nochloro_taxonomy.tsv) is:

OTU	Phylum	Class	Order	Family	Genus	Species
Otu000123	Proteobacteria	Betaproteobacteria	Burkholderiales	betVII	betVII-B	betVII-B1
Otu000027	Proteobacteria	Betaproteobacteria	Burkholderiales	betI	betI-B	Rhodo
Otu000043	Proteobacteria	Betaproteobacteria	Burkholderiales	betI	betI-A	Lhab-A2
Otu000057	Proteobacteria	Betaproteobacteria	Methylophilales	betIV	betIV-A	Unclassified
Otu000176	Proteobacteria	Deltaproteobacteria	Bdellovibrionales	Bacteriovoracaceae	Peredibacter	Unclassified
Otu000005	Cyanobacteria	Cyanobacteria	SubsectionI	FamilyI	Unclassified	Unclassified
Otu000048	Proteobacteria	Alphaproteobacteria	Rhodospirillales	alfVIII	alfVIII_unclassified	Unclassified
Otu000040	Verrucomicrobia	Verrucomicrobia_unclassified	Verrucomicrobia_unclassified	Verrucomicrobia_unclassified	Verrucomicrobia_unclassified	Unclassified
Otu000058	Proteobacteria	Gammaproteobacteria	Methylococcales	gamI	gamI_unclassified	Unclassified
Otu000067	Bacteroidetes	Flavobacteriia	Flavobacteriales	bacII	bacII-A	Unclassified
Otu000029	Bacteroidetes	Cytophagia	Cytophagales	bacIII	bacIII-B	Algor
Otu000025	Bacteroidetes	Cytophagia	Cytophagales	bacIII	bacIII-A	Unclassified

Figure 3